The Summer of Sonic website, a fan-project led by The Sonic Stadium, has gained information that seems to confirm that Amy Rose is set to make an appearance in Sonic the Hedgehog for PS3 and XBOX 360.
In responding to a small set of Q&A questions exclusively for the Summer of Sonic website, arranged by SEGA Europe and TSS, producer Masahiro Kumono (also the new Head of Sonic Team since Yuji Naka's departure) and director Shun Nakamura briefly stated their feelings for the Sonic franchise and where they see it heading after 15 years of popularity.
When asked what Sonic character was their favorite, Kumono-san stated that Amy was a preference, saying that "I like Amy, who appears as an amigo [friend/support] character in this title [Sonic 2006]. She has that same active personality, which build up the story as well as the game."
Not sure if he's actually referring to Sonic 2006, but we'll see. Amy fans, keep your fingers crossed!
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